Is this vehicle under warranty?
A noise such as you describe is usually caused by bearing failure. Could be a trans input shaft bearing or other trans bearing. Bearing failure is almost always caused by improper lubrication or shock load or overheating. ( also mostly due to improper lube)
As far as the window leaks go... do you have ANY LEAKAGE when washing the car or during rain?
If not then it will be difficult to get the window seals replaced under warranty.
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